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Magnesium in PDB 4okj: Crystal Structure of Rnase As From M Tuberculosis

Protein crystallography data

The structure of Crystal Structure of Rnase As From M Tuberculosis, PDB code: 4okj was solved by M.Romano, R.Van De Weerd, F.C.C.Brouwer, G.N.Roviello, R.Lacroix, M.Sparrius, G.Van Den Brink-Van Stempvoort, J.J.Maaskant, A.M.Van Dersar, B.J.Appelmelk, J.J.Geurtsen, R.Berisio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.89 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.424, 77.055, 104.580, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 25.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Rnase As From M Tuberculosis (pdb code 4okj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Rnase As From M Tuberculosis, PDB code: 4okj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4okj

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Magnesium binding site 1 out of 6 in the Crystal Structure of Rnase As From M Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Rnase As From M Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:67.0
occ:1.00
 O A:HOH443 2.3 67.6 1.0
OE1 A:GLU8 3.1 36.7 1.0
O A:PHE9 3.3 30.4 1.0
N A:PHE9 3.4 27.9 1.0
CA A:GLU8 3.8 27.3 1.0
CZ3 A:TRP46 4.1 54.5 1.0
C A:GLU8 4.1 27.3 1.0
CD A:GLU8 4.1 36.2 1.0
CD1 A:PHE9 4.2 30.1 1.0
C A:PHE9 4.2 29.2 1.0
CB A:GLU8 4.2 28.4 1.0
CE1 A:PHE9 4.2 30.4 1.0
CG A:PHE9 4.3 26.0 1.0
CA A:PHE9 4.3 28.4 1.0
CZ A:PHE9 4.4 33.3 1.0
CD2 A:PHE9 4.5 28.7 1.0
CG2 A:VAL51 4.6 40.4 1.0
CE2 A:PHE9 4.6 28.0 1.0
CG2 A:VAL47 4.6 35.0 1.0
O A:THR7 4.7 28.9 1.0
CE3 A:TRP46 4.8 51.2 1.0
CG A:GLU8 4.8 30.8 1.0
CH2 A:TRP46 4.9 55.6 1.0
O A:HOH340 4.9 39.6 1.0
CB A:PHE9 4.9 28.2 1.0
OE2 A:GLU8 5.0 44.5 1.0

Magnesium binding site 2 out of 6 in 4okj

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Magnesium binding site 2 out of 6 in the Crystal Structure of Rnase As From M Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Rnase As From M Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:51.0
occ:1.00
 O A:HOH457 2.2 67.9 1.0
OD1 A:ASP6 2.6 30.9 1.0
O A:THR7 2.6 28.9 1.0
OD1 A:ASP95 2.7 26.1 1.0
O A:HOH443 3.2 67.6 1.0
O A:HOH397 3.3 50.7 1.0
O A:HOH438 3.4 51.8 1.0
OD2 A:ASP95 3.5 30.1 1.0
CG A:ASP95 3.5 26.4 1.0
CG A:ASP6 3.5 33.9 1.0
C A:THR7 3.8 28.9 1.0
OD2 A:ASP6 3.9 35.4 1.0
N A:THR7 4.0 30.0 1.0
OE2 A:GLU8 4.1 44.5 1.0
O A:HOH435 4.2 68.3 1.0
O A:HOH440 4.4 65.8 1.0
CE2 A:PHE9 4.4 28.0 1.0
OG1 A:THR7 4.4 30.1 1.0
CA A:THR7 4.5 28.8 1.0
CD A:GLU8 4.6 36.2 1.0
CB A:ASP6 4.8 28.7 1.0
OE1 A:GLU8 4.8 36.7 1.0
N A:GLU8 4.8 27.7 1.0
C A:ASP6 4.9 29.6 1.0
CA A:ASP6 4.9 29.5 1.0
OD2 A:ASP145 5.0 40.4 0.5
CB A:ASP95 5.0 24.2 1.0

Magnesium binding site 3 out of 6 in 4okj

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Magnesium binding site 3 out of 6 in the Crystal Structure of Rnase As From M Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Rnase As From M Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:39.8
occ:1.00
 O A:HOH438 2.8 51.8 1.0
O A:TYR5 2.9 25.9 1.0
N A:TRP90 3.1 29.6 1.0
OD1 A:ASP145 3.3 23.4 0.5
O A:HOH440 3.3 65.8 1.0
CG A:GLN149 3.6 31.7 1.0
CA A:ALA89 3.7 27.4 1.0
CB A:ALA89 3.8 25.4 1.0
OD1 A:ASP6 3.8 30.9 1.0
O A:TRP90 3.8 34.7 1.0
CB A:ASP6 3.8 28.7 1.0
CB A:TRP90 3.8 31.6 1.0
C A:ALA89 3.9 28.5 1.0
C A:TYR5 3.9 27.0 1.0
CD A:GLN149 3.9 34.4 1.0
CA A:TRP90 3.9 32.5 1.0
CA A:ASP6 4.0 29.5 1.0
OE1 A:GLN149 4.0 37.9 1.0
CG A:ASP145 4.2 32.2 0.5
C A:TRP90 4.3 34.4 1.0
CG A:ASP6 4.3 33.9 1.0
OD2 A:ASP145 4.4 40.4 0.5
N A:ASP6 4.4 27.8 1.0
NE2 A:GLN149 4.8 30.1 1.0
O A:HOH435 4.8 68.3 1.0
CB A:GLN149 4.9 29.6 1.0

Magnesium binding site 4 out of 6 in 4okj

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Magnesium binding site 4 out of 6 in the Crystal Structure of Rnase As From M Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Rnase As From M Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:58.6
occ:1.00
 O B:HOH302 2.0 53.7 1.0
OD2 B:ASP95 2.6 25.5 1.0
O B:TRP90 2.7 35.9 1.0
OD1 B:ASP6 3.1 36.2 1.0
O B:HOH313 3.1 35.7 1.0
O B:HOH378 3.1 53.5 1.0
CG B:ASP95 3.2 27.6 1.0
MG B:MG202 3.4 41.7 1.0
OD1 B:ASP95 3.4 25.6 1.0
O B:VAL91 3.5 32.9 1.0
C B:TRP90 3.9 35.2 1.0
C B:VAL91 4.1 34.7 1.0
CA B:GLY92 4.2 34.1 1.0
CG B:ASP6 4.3 31.9 1.0
CB B:ASP95 4.4 25.1 1.0
N B:GLY92 4.4 34.6 1.0
N B:TRP90 4.4 29.8 1.0
O B:HOH335 4.5 50.9 1.0
CA B:TRP90 4.7 32.9 1.0
CB B:ALA89 4.7 25.6 1.0
CB B:TRP90 4.8 32.8 1.0
N B:VAL91 4.8 35.2 1.0
CB B:ASP6 4.8 28.6 1.0
CA B:ASP6 4.9 27.4 1.0
CA B:VAL91 4.9 34.9 1.0
O B:TYR5 5.0 24.6 1.0

Magnesium binding site 5 out of 6 in 4okj

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Magnesium binding site 5 out of 6 in the Crystal Structure of Rnase As From M Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Rnase As From M Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:41.7
occ:1.00
 OD1 B:ASP95 2.5 25.6 1.0
O B:HOH302 2.5 53.7 1.0
O B:THR7 2.7 28.4 1.0
OD1 B:ASP6 2.9 36.2 1.0
O B:HOH335 3.3 50.9 1.0
CG B:ASP95 3.3 27.6 1.0
OD2 B:ASP95 3.4 25.5 1.0
MG B:MG201 3.4 58.6 1.0
C B:THR7 3.8 28.4 1.0
CG B:ASP6 3.8 31.9 1.0
N B:THR7 4.0 26.8 1.0
CE2 B:PHE9 4.0 31.3 1.0
OG1 B:THR7 4.1 25.4 1.0
OD2 B:ASP6 4.2 36.8 1.0
CA B:THR7 4.4 26.3 1.0
OE2 B:GLU8 4.6 45.3 1.0
CD2 B:PHE9 4.7 32.5 1.0
CZ B:PHE9 4.7 33.1 1.0
CB B:ASP95 4.7 25.1 1.0
N B:GLU8 4.8 28.4 1.0
CB B:THR7 4.9 27.1 1.0
O B:HOH378 4.9 53.5 1.0
CD B:GLU8 5.0 37.8 1.0
C B:ASP6 5.0 26.5 1.0

Magnesium binding site 6 out of 6 in 4okj

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Magnesium binding site 6 out of 6 in the Crystal Structure of Rnase As From M Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Rnase As From M Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:41.6
occ:1.00
 O B:HOH384 2.6 55.1 1.0
OE2 B:GLU37 2.7 44.1 1.0
N B:GLN67 2.9 31.4 1.0
CB B:GLN67 3.3 34.6 1.0
OG B:SER65 3.6 33.9 1.0
N B:ARG66 3.6 31.8 1.0
CA B:GLN67 3.7 33.1 1.0
CB B:SER65 3.8 32.6 1.0
CD B:GLU37 3.8 43.4 1.0
C B:ARG66 3.9 32.2 1.0
O B:HOH386 3.9 54.5 1.0
CA B:ARG66 4.0 31.6 1.0
CB B:ARG66 4.1 30.6 1.0
OE1 B:GLU37 4.3 44.0 1.0
C B:SER65 4.3 32.7 1.0
O B:HOH379 4.5 49.6 1.0
CA B:SER65 4.6 34.2 1.0
CG B:GLN67 4.7 40.6 1.0
C B:GLN67 4.9 31.6 1.0
O B:ARG66 5.0 31.2 1.0

Reference:

M.Romano, R.Van De Weerd, F.C.C.Brouwer, G.N.Roviello, R.Lacroix, M.Sparrius, G.Van Den Brink-Van Stempvoort, J.J.Maaskant, A.M.Van Der Sar, B.J.Appelmelk, J.J.Geurtsen, R.Berisio. Structure and Function of Rnase As, A Polyadenylate-Specific Exoribonuclease Affecting Mycobacterial Virulence in Vivo Structure V. 22 719 2014.
ISSN: ISSN 0969-2126
PubMed: 24704253
DOI: 10.1016/J.STR.2014.01.014
Page generated: Tue Aug 20 00:53:39 2024

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